I am having a problem with one of the site which would not connect so I decided to remove it from the Managed Server panel.

Every time I go there to access the problem site and select it it decides to connect (but it can't connect anyway) so I am not able to remove that site. I also noticed that I no longer have the ability to manage any of the sites for modification if I needed to because when selecting them for medication they too are automatically connecting.

Some questions:
Have you got the latest version of DFTP?
Is the problem you are having new, and it worked ok before?
Have you got a different computer that you can try it on, and does that work?
If you uninstall DFTP, reboot your machine and reinstall, does the problem correct itself? (You won't lose your connections by uninstalling)
If you remove one of the connections (write down the properties first!) and set it up again, does it work?

If you have the same problem with all the servers you manage, I don't think it would be an issue pertaining to the servers. They don't all go wonky just like that. But you could try Filezilla to see if the connection works there.